Done
Edit Type |
cross |
base |
long |
flag |
additional scenarios |
control points |
X |
X |
X |
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|
brainmask |
X |
X |
X |
|
|
wm |
X |
X |
X |
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|
aseg |
X |
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|
|
|
brainfinalsurfs |
X |
X |
X |
|
Edits made to both cross and base transfer to long; remember to create brain.finalsurfs.manedit.mgz files.Surfaces in long initiated from base but take final destination cues from cross. |
seed point, watershed |
X |
|
|
|
|
cw256 |
X |
|
|
|
|
talairach |
|
|
|
|
|
xopts |
|
|
|
|
|
seed point, fill & cut |
|
|
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|
|
Notes
* After editing the base (for wm.mgz and CPs edits), must run both -autorecon2 & -autorecon3 for longitudinal runs to run successfully.
* After editing the cross-sectionals, it is ok to just run -autorecon2 without -autorecon3.
Edit Type |
cross |
base |
long |
flag |
additional scenarios |
control points |
affected base surf; |
affected long surfs |
affected long surfaces. |
|
|
brainmask |
need to delete base and rerun from scratch in order for edits to work |
affected long surfs |
both small and large scale brainmask edits are incorporated as expected. |
|
|
wm added |
edits copied to long when long run from scratch; |
affected long surfs |
edit wm volume, re-run w/ -autorecon2-wm; Result is corrections to wm volume without corresponding change in white surface. |
|
white surface in long is initiated from base, and will only grow outward following wm volume in cross. Will not pull in even if cross wm volume is severely truncated. |
wm removed |
|
|
edit wm volume, re-run w/ -autorecon2-wm; Result is corrections to wm volume without corresponding change in white surface. |
|
white surface in long is initiated from base, and will only grow outward following wm volume in cross. Will not pull in even if cross wm volume is severely truncated. |
aseg |
edits copied to long but changes are unpredictable |
|
|
|
|
brainfinalsurfs |
Remember to copy edited brain.finalsurfs volume to brain.finalsurfs.manedit.mgz , if only this volume edited, re-run using -autorecon3-pial. |
Remember to copy edited brain.finalsurfs volume to brain.finalsurfs.manedit.mgz , if only this volume edited, re-run using -autorecon3-pial. |
Edit the brain.finalsurfs.mgz volume, make a copy of this edited volume to brain.finalsurfs.manedit.mgz;if only this volume edited, re-run using -autorecon3-pial. |
|
Edits must be made in cross and base in order to edit the longitudinal whose errors stem from the cross and base. |
seed point, watershed |
can only adjust wsthresh for cross; |
n/a |
n/a |
|
|
cw256 |
only have to use this flag once w/ recon-all for cross |
n/a |
n/a |
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|
talairach |
|
|
|
|
|
xopts |
|
|
|
|
|
seed point, fill & cut |
|
|
|
|
|
For LCN faculty and staff, this information is also documented here: https://partnershealthcare.sharepoint.com/sites/LCN/SitePages/Longitudinal-Testing.aspx